Variant report

Variant	rs10899797
Chromosome Location	chr10:43879573-43879574
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43878107..43880798-chr10:43952331..43954011,2	K562	blood:
2	chr10:43855647..43857752-chr10:43878006..43881075,3	MCF-7	breast:
3	chr10:43879008..43883052-chr10:43949060..43952010,4	K562	blood:
4	chr10:43879370..43881344-chr10:43930901..43933311,2	MCF-7	breast:
5	chr10:43858972..43861250-chr10:43879046..43881690,2	K562	blood:

Variant related genes	Relation type
ENSG00000243660	Chromatin interaction
ENSG00000252532	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10409	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10793431	0.85[JPT][hapmap]
rs10899794	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10899803	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10899807	0.90[JPT][hapmap]
rs1112959	0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs11238526	0.97[ASN][1000 genomes]
rs11238532	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs11238536	0.90[JPT][hapmap]
rs11238553	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs1126487	0.85[JPT][hapmap]
rs1126709	0.97[ASN][1000 genomes]
rs12220230	0.90[JPT][hapmap]
rs12240317	0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs12245391	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs12250140	0.90[JPT][hapmap]
rs12257917	0.96[ASN][1000 genomes]
rs12260474	0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs13376803	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1416226	0.85[JPT][hapmap]
rs2066044	0.85[JPT][hapmap]
rs2247979	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2247981	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2248335	0.85[JPT][hapmap]
rs2250444	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2252783	0.90[JPT][hapmap]
rs2252785	0.85[JPT][hapmap]
rs2252800	0.96[ASN][1000 genomes]
rs2255967	0.96[ASN][1000 genomes]
rs2259045	0.85[JPT][hapmap]
rs2260200	0.85[JPT][hapmap]
rs2261636	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2265886	0.85[JPT][hapmap]
rs2265887	0.87[ASN][1000 genomes]
rs2265952	0.94[ASN][1000 genomes]
rs2265953	0.83[ASN][1000 genomes]
rs2460558	0.90[ASN][1000 genomes]
rs2492404	0.81[ASN][1000 genomes]
rs2492405	0.85[JPT][hapmap]
rs2492407	0.90[ASN][1000 genomes]
rs2493648	0.85[JPT][hapmap]
rs2819021	0.85[JPT][hapmap]
rs2819032	0.96[ASN][1000 genomes]
rs2819034	0.95[ASN][1000 genomes]
rs2946992	0.90[ASN][1000 genomes]
rs2999286	0.84[ASN][1000 genomes]
rs3000700	0.93[ASN][1000 genomes]
rs3750890	0.85[JPT][hapmap]
rs4597022	0.85[JPT][hapmap]
rs4948726	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs56059584	0.96[ASN][1000 genomes]
rs60739384	0.90[ASN][1000 genomes]
rs61859002	0.89[ASN][1000 genomes]
rs7070029	0.91[ASN][1000 genomes]
rs7070769	0.85[JPT][hapmap]
rs7088430	0.88[ASN][1000 genomes]
rs7905676	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7914140	0.85[JPT][hapmap]
rs7920539	0.85[JPT][hapmap]
rs9422371	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10899797	TF	trans	parietal	SCAN
rs10899797	MARCH8	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43858600-43891000	Weak transcription	Right Atrium	heart
2	chr10:43869000-43880400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr10:43869200-43882000	Weak transcription	Left Ventricle	heart
4	chr10:43869400-43880200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:43870000-43881200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:43870000-43882000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:43870200-43881000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:43870200-43882000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:43870200-43882000	Weak transcription	Brain Substantia Nigra	brain
10	chr10:43870400-43880000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:43870400-43881000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr10:43870400-43881600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr10:43870400-43882000	Weak transcription	Brain Angular Gyrus	brain
14	chr10:43871000-43880400	Weak transcription	Brain Anterior Caudate	brain
15	chr10:43871200-43881600	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:43871400-43880800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:43871600-43880000	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:43871800-43879600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr10:43872200-43880200	Weak transcription	Lung	lung
20	chr10:43872600-43881000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr10:43873200-43880200	Weak transcription	Gastric	stomach
22	chr10:43873200-43880600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr10:43873200-43881200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:43873200-43890200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr10:43873400-43880800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr10:43873400-43881000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr10:43873400-43881000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr10:43873400-43881000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:43873400-43881200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr10:43873400-43881400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr10:43873400-43881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr10:43873400-43882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:43873400-43891000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr10:43873800-43881000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:43873800-43881000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr10:43873800-43882000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr10:43873800-43882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:43874400-43882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr10:43876000-43879600	Weak transcription	Fetal Stomach	stomach
40	chr10:43876000-43881800	Weak transcription	Colon Smooth Muscle	Colon
41	chr10:43876200-43880000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr10:43876600-43880200	Weak transcription	Dnd41	blood
43	chr10:43876600-43880400	Weak transcription	Hela-S3	cervix
44	chr10:43876800-43880200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr10:43876800-43880200	Weak transcription	NHLF	lung
46	chr10:43877000-43880000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr10:43877000-43880000	Weak transcription	HSMMtube	muscle
48	chr10:43877000-43880200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr10:43877000-43880600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr10:43877200-43880400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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